SalmoBase

Genomic data resource with genome browsers, BLAST search, and gene assemblies for Atlantic salmon and salmonid species.

Overview

SalmoBase is a genomic data resource for Atlantic salmon and other salmonid species, developed as part of ELIXIR Norway. It provides genome browsers, gene assemblies, and sequence search tools, making molecular genomic resources for salmonids publicly available through integrated visualization and analysis frameworks. SalmoBase is the sister database of LiceBase, which focuses on salmon lice genomics.

Salmonids encompass 11 genera and at least 70 species, including Atlantic salmon, rainbow trout, whitefishes, graylings, and char. Their common ancestor underwent a whole genome duplication (WGD) approximately 80 million years ago, producing an autotetraploid genome. Ongoing genomic rediploidization makes salmonids a distinct system for studying the evolutionary consequences of WGD.

Key Features

Genome browser — interactive browsing of salmonid species genomes via JBrowse
BLAST search — querying salmonid genomic and protein sequences against reference databases
SalMotifDB — access to transcription factor binding motifs specific to salmonid species
Gene assemblies — exploration of specific gene assemblies across multiple salmonid species
High-quality reference sequences — includes established genome sequences for Atlantic salmon and rainbow trout
Continuous updates — new genomic resources are added as they become publicly available

Getting Started

Visit SalmoBase to explore available species and datasets
Use the genome browser to navigate chromosomal regions of interest
Run BLAST searches to find homologous sequences across salmonid genomes
Access SalMotifDB for transcription factor binding site data

SalmoBase is hosted under ELIXIR Norway and is publicly accessible. It is linked to LiceBase, a sister database covering salmon lice genomics, providing complementary resources for researchers working across salmonid biology.